Lattice Light-Sheet | Organoids | ML and Big Data | Optical Tweezing | Reaction-Diffusion | Fun

Publications | Git | CV | Teaching | Open Positions

Welcome!

Enjoy browsing my science!

4D Lattice Light-Sheet Organoid Imaging

I use endogenously GFP/RFP tagged stem cells to grow tissues (organoids) and then image them live with the lattice light-sheet microscope (LLSM). Shown below is a young brain organoid and a polarized intestinal organoid. LLSM imaging is done at superresolution with seconds frame rates. The resulting large datasets (terabytes) are analyzed using my custom analysis software pyLattice.

J Schöneberg, D Dambournet, T-L Liu, R Forster, D Hockemeyer, E Betzig, D G Drubin (2018) 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids. Molecular Biology of the Cell, 29(24).

pyLattice - Machine Learning-based Lattice Light-Sheet Data Analytics

pyLattice is a python library for advanced lattice light-sheet image analysis. Collaborate with us on gitHub and read about how we solve big data analytics challenges when we analyze big LLSM datasets.

J Schöneberg, G Raghupathi, E Betzig, D G Drubin (2019) 3D Deep Convolutional Neural Networks in Lattice Light-Sheet Data Puncta Segmentation. IEEE Proceedings International Conference on Bioinformatics and Biomedicine (BIBM), in press.

Scope Engineering and Optical Tweezing

I combined confocal microscopy with optical trapping to measure force and fluorescence of proteins acting on small membrane nanotubes (pulled from e.g. a giant unilamellar vesicles (GUV)). These nanotubes allow studying protein-membrane biophysics in tubular, highly curved topologies. They resemble vesicle necks found e.g. in normal topology budding (e.g. Clathrin mediated endocytosis) and reverse topology budding (ESCRT system).

The Confleezers: Left:The Confleezers 1.0 that combines confocal microscopy with optical tweezing. Right: Membrane nanotubes pulled from model membranes using micromanipulators (top) and the trap of the Confleezers (bottom).

See our applications on the ESCRT system and our review:

J Schöneberg, M R Pavlin*, S Yan*, M Righini, I-H Lee, L-A Carlson, A H Bahrami, D H Goldman, X Ren, G Hummer, C Bustamante and J H Hurley (2018) ATP-dependent force generation and membrane scission by ESCRT-III and Vps4, Science, 362 (6421), 1423-1428. * equal contribution.

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteins. Nature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).

Reaction-Diffusion

https://www.nature.com/articles/ncomms15873

J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, V Haucke, F Noé, (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications 8, 15873 doi: 10.1038/ncomms15873. (*equal contribution).

See our contributions to the rod cell visual cascade: Structure 2015: Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Biophysical Journal 2014: Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes.

ReaDDy

ReaDDy is a particle-based reaction-diffusion simulation software. It features

simulation in and on arbitrary geometries (i.e. 3D, 2D, spherical,...),
spatial confinement (walls, boxes, tubes, ...),
excluded volume of particles (crowding effects) and
particle-particle interaction potentials (repulsion, attraction, clustering, ...).

See more under readdy-project.org, contribute under gitHub/readdy and read the paper under Schöneberg and Noé, PLOS ONE, 2013. Also check out the newest ReaDDy developments here.

Links

In MCB at UC Berkeley, I currently work in the Drubin, Hockemeyer and Betzig labs. I have worked in the Hurley, Bustamante and Hummer labs. Download pyLattice and ReaDDy and collaborate with us on gitHub.